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PubMed2026

Genomic exploration of Bacillus paralicheniformis TB197: an agrobiotechnological tool from the Sonoran Desert.

Climate change and the harmful effects of extensive agrochemical use for plant nutrition and pest control on soils, the environment, and human health are driving the search for sustainable alternatives that reduce their use while increasing plant resilience. In regenerative agriculture, microorganisms have become valuable tools, acting as biological control agents or biostimulants, such as plant growth-promoting rhizobacteria, and/or to enhance plant performance under abiotic stress. The genus Bacillus is well known for its versatile interactions with plants. Specifically, Bacillus paralicheniformis TB197 has demonstrated high efficacy in controlling phytopathogenic nematodes and adapting to diverse soil and crop conditions. Based on these traits, we explored the agricultural potential of this strain through genomic analysis and in vitro and in vivo assays. Gene analysis identified functions related to three main areas: (i) stress resistance and plant colonization, (ii) plant growth promotion, and (iii) phytopathogen control. The strain showed high tolerance to salinity and temperature, promoted plant growth, and exhibited strong antifungal activity. These findings highlight the potential of the TB197 strain as a promising candidate for developing next-generation bioinoculants.IMPORTANCEThe use of beneficial microorganisms is a pivotal strategy for mitigating the environmental impacts of intensive agriculture while preserving crop productivity. Bacillus paralicheniformis TB197 is a native desert soil bacterium with genetic traits associated with stress tolerance, plant growth promotion, and suppression of plant pathogens. In this study, we employed a multifaceted approach integrating genomic analysis and functional assays to demonstrate the strain's multifunctional potential as an agricultural bioinoculant. The results of the study demonstrate that a singular bacterial strain can integrate multiple beneficial functions relevant to sustainable agriculture. This work contributes to the field of applied microbiology by expanding the understanding of how environmentally adapted bacteria can serve as biological alternatives to chemical inputs in agroecosystems.

Bacillus↗
PubMed2002

Melanin-concentrating hormone and its receptors: state of the art.

Melanin-concentrating hormone (MCH) is a cyclic neuropeptide of nineteen amino acids in mammals. Its involvement in the feeding behaviour has been well established during the last few years. A first receptor subtype, now termed MCHIR, was discovered in 1999, following the desorphanisation of the SLCI orphan receptor, using either reverse pharmacology or systematic screening of agonist candidates. A second MCH receptor, MCH2R, has been discovered recently, by several groups working on data mining of genomic banks. The molecular pharmacology of these two receptors is only described on the basis of the action of peptides derived from MCH. The present review tentatively summarizes the knowledge on these two receptors and presents the first attempts to discover new classes of antagonists that might have major roles in the control of obesity and feeding behaviour.

Amino Acid Sequence↗
PubMed2000

Banking biological collections: data warehousing, data mining, and data dilemmas in genomics and global health policy.

While DNA databases may offer the opportunity to (1) assess population-based prevalence of specific genes and variants, (2) simplify the search for molecular markers, (3) improve targeted drug discovery and development for disease management, (4) refine strategies for disease prevention, and (5) provide the data necessary for evidence-based decision-making, serious scientific and social questions remain. Whether samples are identified, coded, or anonymous, biological banking raises profound ethical and legal issues pertaining to access, informed consent, privacy and confidentiality of genomic information, civil liberties, patenting, and proprietary rights. This paper provides an overview of key policy issues and questions pertaining to biological banking, with a focus on developments in specimen collection, transnational distribution, and public health and academic-industry research alliances. It highlights the challenges posed by the commercialization of genomics, and proposes the need for harmonization of biological banking policies.

Databases, Nucleic Acid↗
PubMed2025

Uncovering encrypted antimicrobial peptides in health-associated Lactobacillaceae by large-scale genomics and machine learning.

BACKGROUND: Antimicrobial peptides (AMPs) are well known for their broad-spectrum activity and have shown great promise in addressing the antibiotic-resistant crisis. The Lactobacillaceae family, recognized for its health-promoting effects in humans, represents a valuable source of novel AMPs. However, the global prevalence and distribution of AMPs within Lactobacillaceae remains largely unknown, which limits the efficient discovery and development of novel AMPs. RESULTS: We analyzed all available genomes (10,327 genomes), encompassing 38 genera and 515 species, to investigate the biosynthetic potential (indicated by the number of AMP sequences in the genome) of AMP in the Lactobacillaceae family. We demonstrated Lactobacillaceae species had ubiquitous (69.90%) biosynthetic potential of AMPs. Overall, 9601 AMPs were identified, clustering into 2092 gene cluster families (GCFs), which showed strong interspecies specificity (95.27%), intraspecies heterogeneity (93.31%), and habitat uniqueness (95.83%), that greatly expanded on the AMP sequence landscape. Novelty assessment indicated that 1516 GCFs (72.47%) had no similarity to any known AMPs in existing databases. Machine learning predictions suggested that novel AMPs from Lactobacillaceae possessed strong antimicrobial potential, with 664 GCFs having an additive minimum inhibitory concentration (MIC) below 100&#xa0;&#x3bc;M. We randomly synthesized 16 AMPs (with predicted MIC&#x2009;<&#x2009;100&#xa0;&#x3bc;M) and identified 10 AMPs exhibiting varied-spectrum activity against 11 common pathogens. Finally, we identified one Lactobacillus delbrueckii-originated AMP (delbruin_1) having broad-spectrum (all 11 pathogens) and high antimicrobial activity (average MIC&#x2009;=&#x2009;38.56 &#xb5;M), which proved its potential as a clinically viable antimicrobial agent. CONCLUSIONS: We uncovered the global prevalence of AMPs in Lactobacillaceae and proved that Lactobacillaceae is an untapped and invaluable source of novel AMPs to combat the antibiotic-resistance crisis. Meanwhile, we provided a machine learning-guided framework for AMP discovery, offering a scalable roadmap for identifying novel AMPs not only in Lactobacillaceae but also in other organisms. Video Abstract.

Machine Learning↗
PubMed2004

New approaches to development of mucosal vaccine against enteric bacterial pathogens; preventing campylobacteriosis.

Although vaccination, after having been more than 200 years in medical practice, has proven to be the most effective and the cheapest way to prevent infectious diseases, they remain still the main cause of human premature deaths. As many pathogens enter the human body through the mucosal surfaces, the mucosal way of immunization is considered to be the most promising strategy to decrease the number of human infections. Moreover, the oral delivery system eliminates the necessity of injection what is extremely important for pediatric immunization programs. However, most of recently constructed subunit vaccines based on purified bacterial/viral antigens are rather poorly immunogenic. This review presents some novel ways to enhance and modulate host immune responses by combining antigens with specific adjuvants or by employing specific delivery systems. We also discuss some recent technologies, based on mining the genomic sequences of bacterial pathogens, which accelarate and improve identification of new candidates for vaccine construction. As an example, we focus on the progress in the development of vaccine against Campylobacter spp. Campylobacter jejuni is now recognized as a leading cause of bacterial enteritis in human.

Adjuvants, Immunologic↗
PubMed1997

Data mining for regulatory elements in yeast genome.

We have examined methods and developed a general software tool for finding and analyzing combinations of transcription factor binding sites that occur relatively often in gene upstream regions (putative promoter regions) in the yeast genome. Such frequently occurring combinations may be essential parts of possible promoter classes. The regions upstream to all genes were first isolated from the yeast genome database MIPS using the information in the annotation files of the database. The ones that do not overlap with coding regions were chosen for further studies. Next, all occurrences of the yeast transcription factor binding sites, as given in the IMD database, were located in the genome and in the selected regions in particular. Finally, by using a general purpose data mining software in combination with our own software, which parametrizes the search, we can find the combinations of binding sites that occur in the upstream regions more frequently than would be expected on the basis of the frequency of individual sites. The procedure also finds so-called association rules present in such combinations. The developed tool is available for use through the WWW.

Binding Sites↗
PubMed2005

Farm animal genomics and informatics: an update.

Farm animal genomics is of interest to a wide audience of researchers because of the utility derived from understanding how genomics and proteomics function in various organisms. Applications such as xenotransplantation, increased livestock productivity, bioengineering new materials, products and even fabrics are several reasons for thriving farm animal genome activity. Currently mined in rapidly growing data warehouses, completed genomes of chicken, fish and cows are available but are largely stored in decentralized data repositories. In this paper, we provide an informatics primer on farm animal bioinformatics and genome project resources which drive attention to the most recent advances in the field. We hope to provide individuals in biotechnology and in the farming industry with information on resources and updates concerning farm animal genome projects.

Animals↗
PubMed2001

Discovery of a novel murine type C retrovirus by data mining.

Analysis of genomic and expression data allows both identification and characterization of novel retroviruses. We describe a recombinant type C murine retrovirus, similar to the Mus dunni endogenous retrovirus, with VL30-like long terminal repeats and murine leukemia virus-like coding sequences. This virus is present in multiple copies in the mouse genome and expressed in a range of mouse tissues.

Amino Acid Sequence↗
PubMed2005

Key enzymes of the protocatechuate branch of the beta-ketoadipate pathway for aromatic degradation in Corynebacterium glutamicum.

Although the protocatechuate branch of the beta-ketoadipate pathway in Gram+ bacteria has been well studied, this branch is less understood in Gram+ bacteria. In this study, Corynebacterium glutamicum was cultivated with protocatechuate, p-cresol, vanillate and 4-hydroxybenzoate as sole carbon and energy sources for growth. Enzymatic assays indicated that growing cells on these aromatic compounds exhibited protocatechuate 3,4-dioxygenase activities. Data-mining of the genome of this bacterium revealed that the genetic locus ncg12314-ncg12315 encoded a putative protocatechuate 3,4-dioxygenase. The genes, ncg12314 and ncg12315, were amplified by PCR technique and were cloned into plasmid (pET21aP34D). Recombinant Escherichia coli strain harboring this plasmid actively expressed protocatechuate 3,4-dioxygenase activity. Further, when this locus was disrupted in C. glutamicum, the ability to degrade and assimilate protocatechuate, p-cresol, vanillate or 4-hydroxybenzoate was lost and protocatechuate 3,4-dioxygenase activity was disappeared. The ability to grow with these aromatic compounds and protocatechuate 3,4-dioxygenase activity of C. glutamicum mutant could be restored by gene complementation. Thus, it is clear that the key enzyme for ring-cleavage, protocatechuate 3,4-dioxygenase, was encoded by ncg12314 and ncg12315. The additional genes involved in the protocatechuate branch of the beta-ketoadipate pathway were identified by mining the genome data publically available in the GenBank. The functional identification of genes and their unique organization in C. glutamicum provided new insight into the genetic diversity of aromatic compound degradation.

Adipates↗
PubMed2005

Bioinformatic analysis of peptide precursor proteins.

Neuropeptides are among the most important signal molecules in animals. Traditional identification of peptide hormones through peptide purification is a tedious and time-consuming process. With the advent of the genome sequencing projects, putative peptide precursor can be mined from the genome. However, because bioactive peptides are usually quite short in length and because the active core of a peptide is often limited to only a few amino acids, using the BLAST search engine to identify neuropeptide precursors in the genome is difficult and sometimes impossible. To overcome these shortcomings, we subject the entire set of all known Drosophila melanogaster peptide precursor sequences to motif-finding algorithms in search of a motif that is common for all prepropeptides and that could be used in the search for new peptide precursors.

Amino Acid Sequence↗
PubMed2026

Isolation, genomic characterization, and safety assessment of an O-desmethylangolensin-producing Clostridium beijerinckii strain from Chinese Stinky Tofu.

The health benefits of dietary soy isoflavones are largely mediated by specific microbial metabolites, such as O-desmethylangolensin (O-DMA). However, the diversity and application potential of O-DMA-producing strains remain poorly explored, primarily due to the limited availability of isolated strains, narrow ecological sources, and a lack of practical applications. In this study, an O-DMA-producing bacterium, designated strain FRJF5, was isolated from Chinese stinky tofu under anaerobic conditions and was identified as Clostridium beijerinckii. The biosynthesized O-DMA exhibited an enantiomeric excess (e.e.) of 78.6%. Based on phylogenetic and average nucleotide identity analyses against 235 public C. beijerinckii genomes, the clustering of FRJF5 with strains from diverse habitats-including industrial fermentation settings, animal feces, and soil-highlights the broad ecological diversity within this species. Functional gene mining and intra-species comparative genomics revealed a unique flavonoid metabolism gene cluster in FRJF5. Using apigenin as a representative flavonoid, we confirmed the successful conversion to 3-(4-hydroxyphenyl)-propionic acid. Moreover, the strain was predicted and verified to possess a substantial butyrate-producing capacity. Genomic screening for virulence or antibiotic resistance genes, combined with phenotypic tests (hemolysis, antibiotic susceptibility, and mouse gavage), revealed a favorable safety profile for strain FRJF5. Finally, intervention experiments in a mouse model of colitis supported its potential in alleviating the disease. Collectively, this study identifies C. beijerinckii FRJF5 as a strain capable of simultaneously producing O-DMA and butyrate, highlighting its potential for future applications in functional foods.IMPORTANCESoy isoflavones require gut bacterial conversion into bioactive metabolites-such as the anti-inflammatory compound O-desmethylangolensin (O-DMA)-to exert health benefits. Yet O-DMA-producing strains remain scarce, largely confined to fecal sources, and poorly characterized. Here, we isolated Clostridium beijerinckii FRJF5 from Chinese stinky tofu, an unexplored ecological niche. This strain not only produces enantiomerically enriched O-DMA but also co-produces butyrate, a metabolite known to strengthen gut barrier function. Genomic mining uncovered a unique flavonoid metabolism gene cluster responsible for this dual activity. Combined with favorable safety profiles, FRJF5 emerges as a strong candidate for functional food applications. This work expands the known diversity of O-DMA producers and bridges traditional fermented foods with next-generation probiotic development.

O-desmethylangolensin↗
PubMed2003

Mining the biomedical literature in the genomic era: an overview.

The past decade has seen a tremendous growth in the amount of experimental and computational biomedical data, specifically in the areas of genomics and proteomics. This growth is accompanied by an accelerated increase in the number of biomedical publications discussing the findings. In the last few years, there has been a lot of interest within the scientific community in literature-mining tools to help sort through this abundance of literature and find the nuggets of information most relevant and useful for specific analysis tasks. This paper provides a road map to the various literature-mining methods, both in general and within bioinformatics. It surveys the disciplines involved in unstructured-text analysis, categorizes current work in biomedical literature mining with respect to these disciplines, and provides examples of text analysis methods applied towards meeting some of the current challenges in bioinformatics.

Biomedical Research↗
PubMed2006

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed.

Animals↗
PubMed2003

Genomic characterization of Rim2/Hipa elements reveals a CACTA-like transposon superfamily with unique features in the rice genome.

The availability of huge amounts of rice genome sequence now permits large-scale analysis of the structure and molecular characteristics of the previously identified transposase-encoding Rim2 (also called Hipa) element, which is transcriptionally activated by infection with the fungal pathogen Magnaporthe grisea and by treatment with the corresponding fungal elicitor. Based on genomic cloning and data mining from 230 Mb of rice genome sequence, 347 Rim2 elements, with an average size of 5.8 kb, were identified. This indicates that an estimated total of 600-700 Rim2 elements are present in the whole genome. Rim2 insertions occur non-randomly on the chromosomes, as visualized by fluorescence in situ hybridization. The elements harbor 16-bp terminal inverted repeats with the core sequence CACTG, 16-bp sub-terminal repeats, internal variable regions, 3-bp target sequence duplications in the flanking regions, and genes coding for Rim2 proteins (the putative transposase) and hydroxyproline-rich glycoproteins. High levels of insertion into genic regions are observed for members of this family, and the transposition history of the family can be deduced from the high level of shared sequences and analysis of repeat target sites of the elements. Phylogenetic analysis indicates that the putative RIM2 proteins fall into a subgroup distinct from the TNP2-like subgroup of transposases. Southern hybridization with genomic DNA from monocotyledonous and dicotyledonous plants demonstrates that the RIM2-coding sequence is unique to the Oryza genome. Our results demonstrate that the Rim2 elements from rice belong to a distinct superfamily of CACTA-like elements with evolutionary diversity.

Amino Acid Sequence↗
PubMed1999

Knowledge discovery in gene-expression-microarray data: mining the information output of the genome.

A key aspect of the genomics revolution is the transformation of large amounts of biological information into an electronic format, leading to an information-based approach to biomedical problems. Large-scale RNA assays and gene-expression-microarray studies, in particular, represent the second wave of the genomics revolution, providing gene-expression data that complement gene-sequence data and help our understanding of the molecular basis of health and disease. They are being applied at several stages in the drug-development process and could ultimately have broad applications in disease diagnosis and patient prognosis.

Animals↗
PubMed2004

Cloning of a novel neuronally expressed orphan G-protein-coupled receptor which is up-regulated by erythropoietin, interacts with microtubule-associated protein 1b and colocalizes with the 5-hydroxytryptamine 2a receptor.

G-protein-coupled receptors (GPCRs) are the largest group of cell surface molecules involved in signal transduction and are receptors for a wide variety of stimuli ranging from light, calcium and odourants to biogenic amines and peptides. It is assumed that systematic genomic data-mining has identified the overwhelming majority of all remaining GPCRs in the genome. Here we report the cloning of a novel orphan GPCR which was identified in a search for erythropoietin-induced genes in the brain as a strongly up-regulated gene. This unknown gene coded for a protein which had a seven-transmembrane topology and key features typical of GPCRs of the A family but a low overall identity to all known GPCRs. The protein, coded ee3, has an unusually high evolutionary conservation and is expressed in neurons in diverse areas of the CNS with relation to integrative functions or motor tasks. A yeast two-hybrid screen for interacting proteins revealed binding to the microtubule-associated protein (MAP) 1b. Coupling to MAP1a has been described for another cognate GPCR, the 5-hydroxytryptamine (5HT) 2a receptor. Surprisingly, we found complete colocalization of ee3 and the 5HT2a receptor. The interaction with MAP1b proved to be critical for the stability or folding of ee3 as in mice lacking MAP1b the ee3 protein was undetectable by immunohistochemistry, although messenger RNA levels remained unchanged. We propose that ee3 is a highly interesting new orphan GPCR with potential connections to erythropoietin and 5HT2a receptor signalling.

Amino Acid Sequence↗
PubMed2006

Novel strategies to identify relevant molecular signatures for complex human diseases based on data of identical-by-decent profiles and genomic context.

OBJECTIVE: To develop novel strategies to identify relevant molecular signatures for complex human diseases based on data of identical-by-decent profiles and genomic context. METHODS: In the proposed strategies, we define four relevancy criteria for mapping SNP-phenotype relationships-point-wise IBD mean difference, averaged IBD difference for window, Z curve and averaged slope for window. RESULTS: Application of these criteria and permutation test to 100 simulated replicates for two hypothetical American populations to extract the relevant SNPs for alcoholism based on sib-pair IBD profiles of pedigrees demonstrates that the proposed strategies have successfully identified most of the simulated true loci. CONCLUSION: The data mining practice implies that IBD statistic and genomic context could be used as the informatics for locating the underlying genes for complex human diseases. Compared with the classical Haseman-Elston sib-pair regression method, the proposed strategies are more efficient for large-scale genomic mining.

Alcoholism↗